RNA Seq of NCC2705 grown on glucose replicate 1
The Prokarotic AnyDeplete workflow is as follows: 250 ng of total RNA was used as input to produce cDNA, followed by an enzymatic fragmentation to a target size of around 200pb. End-repair of the cDNA was performed, and specific adaptors provided with the kit (8 bases index allowing sample multiplexing for Illumina sequencing) were added by ligation. A strand selection step (to retain RNA strand information) was followed by a ribodepletion step aiming at eliminating unwanted rRNA transcript sequences. Finally, 18 PCR cycles were used for the final amplification of the libraries using specific primers provided in the AnyDeplete kit. Obtained DNA fragments were then purified with a 1:1 ratio of AMPURE XP beads (Beckman Coulter Life Sciences, Indianapolis, USA). Libraries were checked on a Labchip GX touch with DNA High Sensitivity Reagent Kit (PerlinElmer Inc., Waltham, USA). All samples were finally sequenced on an Illumina HiSeq 2500 with Rapid V2 chemistry (Illumina Inc., San Siego, USA), applying 200 cycles (paired-end reads PE100). Flowcell was loaded with 10 pM of DNA and with 2% PhiX control v3 library (internal control enabling quality check of the sequencing run; Illumina Inc.).